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Merge branch 'master' into get_tbi_files_from_gatk4_mergevcfs
This commit is contained in:
FriederikeHanssen
GitHub
commit
19037ed8f4
8 changed files with 45 additions and 15 deletions
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@ -42,7 +42,6 @@ output:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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## TODO nf-core: Delete / customise this example output
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- out:
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type: file
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description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)
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@ -8,7 +8,7 @@ process BCFTOOLS_CONCAT {
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'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
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input:
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tuple val(meta), path(vcfs)
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tuple val(meta), path(vcfs), path(tbi)
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output:
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tuple val(meta), path("*.gz"), emit: vcf
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@ -25,6 +25,11 @@ input:
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description: |
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List containing 2 or more vcf files
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e.g. [ 'file1.vcf', 'file2.vcf' ]
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- tbi:
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type: files
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description: |
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List containing 2 or more index files (optional)
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e.g. [ 'file1.tbi', 'file2.tbi' ]
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output:
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- meta:
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type: map
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@ -20,7 +20,7 @@ process FILTLONG {
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
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def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
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"""
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filtlong \\
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$short_reads \\
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@ -4,13 +4,25 @@ nextflow.enable.dsl = 2
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include { BCFTOOLS_CONCAT } from '../../../../modules/bcftools/concat/main.nf'
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workflow test_bcftools_concat {
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workflow test_bcftools_concat_tbi {
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input = [ [ id:'test3' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ]
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file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) ]
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]
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BCFTOOLS_CONCAT ( input )
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}
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workflow test_bcftools_concat_no_tbi {
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input = [ [ id:'test3' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
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[]
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]
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BCFTOOLS_CONCAT ( input )
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}
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@ -1,8 +1,17 @@
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- name: bcftools concat test_bcftools_concat
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command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
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- name: bcftools concat test_bcftools_concat_tbi
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command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
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tags:
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- bcftools/concat
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- bcftools
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- bcftools/concat
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files:
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- path: output/bcftools/test3.vcf.gz
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md5sum: 35c88bfaad20101062e98beb217d7137
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- name: bcftools concat test_bcftools_concat_no_tbi
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command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
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tags:
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- bcftools
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- bcftools/concat
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files:
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- path: output/bcftools/test3.vcf.gz
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md5sum: 35c88bfaad20101062e98beb217d7137
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@ -2,4 +2,6 @@ process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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ext.args = "--min_length 10"
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}
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@ -4,7 +4,8 @@
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- filtlong
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files:
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- path: output/filtlong/test_lr_filtlong.fastq.gz
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md5sum: 7029066c27ac6f5ef18d660d5741979a
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contains:
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- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
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- name: filtlong test_filtlong_illumina_se
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command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
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@ -12,7 +13,8 @@
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- filtlong
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files:
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- path: output/filtlong/test_lr_filtlong.fastq.gz
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md5sum: 7029066c27ac6f5ef18d660d5741979a
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contains:
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- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
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- name: filtlong test_filtlong_illumina_pe
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command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
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@ -20,4 +22,5 @@
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- filtlong
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files:
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- path: output/filtlong/test_lr_filtlong.fastq.gz
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md5sum: 7029066c27ac6f5ef18d660d5741979a
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contains:
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- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
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